Flying vs Ferry

Since you will be at the airport, I would take the most convenient flight. During our visit to Greece, there was a one day ferry strike which required last minute travel adjustment with a mad dash to the airport. Save yourself the hassle of leaving the airport and going to the ferry port.

Ewww, that's a factor I never thought of. Thank you!

Since you are at the airport, I'd say fly. However, it's tough to buy a non-refundable ticket as you don't know if your arriving flight into Athens will be on time.

What islands are you thinking of? I will say that Crete, Santorini, Rhodes, and a few others, almost always make sense to fly to rather than take a ferry for hours and hours. If you are doing several islands, fly to the furthest one, and work your way back by ferry.

Leave yourself a buffer of several hours, as Frank implied, have a plan B in case you have a serious delay and lose your ticket value.

What airline are you flying? Aegean/Olympic is part of the Star alliance, so if United, you should be able to get a single ticket to your island, guaranteeing passage. Either way, I would still price a single ticket, it may not be much more than fare to Athens plus separate tickets, so cheap insurance.

Don't bother looking, the only ferries worth taking to experience the Greek islands are the traditional ones. They leave the port of Piraeus too early in the morning (between 7:00 and 8:30 AM) to catch one when you arrive at Athens airport.

The high-speed ferries make two round trips a day, and their second departure from the port of Piraeus is around 2:30-3:30 PM, so you probably won't be able to catch one either.

So no regrets. Just take a flight since the island you're considering has an airport.

With a single ticket, coming from a Schengen country, I've sometimes had a layover of less than 40 minutes at Athens airport for a flight to an island. If you can get a flight on a single ticket, as Paul mentioned, that's even better. But it's quite rare.
So, coming from the USA, allow at least 2.5 hours in Athens for your connection between flights; 3 hours is even better to be safe in case of any unforeseen problems.

If you want to take a ferry, you can do so on the return trip. It's like a rite of passage into adulthood in some cultures, you'll be considered a true traveler in the Greek islands. :)

But take a traditional ferry like those operated by Blue Star Ferries and avoid the Seajets high-speed catamarans which are certainly faster, but also more expensive and less enjoyable.

Ferry strikes are less frequent than sailing bans due to weather conditions. When there's a strike, you'll know at least several days in advance. If there are no ferries due to bad weather, you won't know until the day before departure at the earliest.

Thanks all for your feedback. The flight that I'm eyeing lands in Athens at 9:15am. I wouldn't make the connection tight. I would probably get an early afternoon flight to give us plenty of time. I may re-start my search and see about buying one ticket (even if that means switching from American).
I'm looking at Milos, Kefalonia, Naxos, Paros, Karpathos, or Crete. We are not island hopping. We are going to choose only one for four nights, then Athens for four nights. (We have an 8 day cruise that will visit Santorini, Mykonos, and Rhodes.) I know that Crete is really accessible due to its size, but I'm not sure I want to go to such a big island... So many decisions!
JoLiu, I'd like to take a ferry back to Athens when we leave the island. I'd prefer that over the hassle of flying! Plus, I love a good boat ride! :D

Kefalonia and Karpathos don't have direct Athens ferries. They are in different island groups than the Cyclades Islands. Crete is the farthest by ferry from Athens in the Cyclades.

Karpathos does not have direct ferries to Athens.

The Blue Star Chios operates the Piraeus-Karpathos route in both directions 3 times a week, year-round (12-hour journey, mostly overnight).

Just to give you all an update, I took the advice above and ended up booking our flight through to Chania, Crete on one ticket. I appreciate that advice. I realized that none of the flights I looked at even go through Athens. We will actually be flying through Helsinki! And I saw that the ferry journeys are LONG to get from Crete to Athens, so we'll just be flying. I wanted to do a ferry somewhere, and that's still a possibility for day trips, but certainly not getting to Athens! Thanks again all. You changed the way we were going to start the trip -- for the better. You probably saved us time, stress, and money!

If you want a do-able day trip from Athens that will give you a "ferry experience" I can recommend going to AEGINA which is just an hour from Piraeus port -- so close that many "commute" to Athens jobs. Two Important tips:
(1) catch a conventional open-deck ferry, not a hydrofoil, with inside-only seats; almost no view.
(2)for serene visit, go M-F, because Athenians flock there on weekends.
Theres a ticket agency almost every block in central athens. Go the night before, check timetable & get tickets. Both Green Line and Blue Line Metros go to Piraeus terminal right across street from ferry slips.

This photo-sequence -- https://www.flickr.com/photos/36264706@N03/sets/72157621604646139/detail/ -- shows a June day-trip, but the weather is very enjoyable, and water very swimmable, in September. As it shows you can enjoy "mini-cruise", seeing huge freighters, sleek speedboats, 3-masted schooners.

THose pix suggest an itinerary by car. You can also rent ebikes... very do-able on main central road (not that busy weekdays), & also a (not too frequent) bus. I took a bus to the stunning Intact ancient temple atop a hill in center, 360° view of Saronic bay... then found a shortcut path to Ag Marina beach for a swim, lunch then bus back to port. Of curse, if you want to rent a car, you can go much further afield, but this wa nice as a one-day sampling. The port town is not that touristic, fascinating to roam back streets & browse in shops for what locals buy for meals & home decor. Then an adult beverage at a seafront cafe, anad a sunset sail back to Athens for dinner.